Excessive phosphorus loading to inland freshwater lakes around the globe has resulted in nuisance plant growth along the waterfronts, degraded habitat for cold water fisheries, and impaired beaches, marinas and waterfront property. This novel study presents a first-time application of the Genetic Algorithm methodology to optimize the application of best management practices related to agriculture and mobile sources to achieve atmospheric phosphorus reduction targets and restore the ecological health of the lake. The novel methodology takes into account the spatial distribution of the emission sources in the airshed, the complex atmospheric long-range transport and deposition processes, cost and efficiency of the popular management practices and social constraints related to the adoption of BMPs.